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- PDB-5ffq: ChuY: An Anaerobillin Reductase from Escherichia coli O157:H7 -

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Basic information

Entry
Database: PDB / ID: 5ffq
TitleChuY: An Anaerobillin Reductase from Escherichia coli O157:H7
ComponentsShuY-like protein
KeywordsUNKNOWN FUNCTION / NADPH oxidoreductase
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding domain superfamily / 1,4-BUTANEDIOL / PHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLaMattina, J.W. / Reedy, A.N. / Uy, K.G. / Lanzilotta, W.N.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Radical new paradigm for heme degradation in Escherichia coli O157:H7.
Authors: LaMattina, J.W. / Nix, D.B. / Lanzilotta, W.N.
History
DepositionDec 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ShuY-like protein
B: ShuY-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9525
Polymers43,6722
Non-polymers2803
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-11 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.486, 63.201, 66.535
Angle α, β, γ (deg.)90.00, 106.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ShuY-like protein / Uncharacterized protein


Mass: 21835.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: chuY, ECs4385, Z4917 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8X5N4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Bis Tris pH 5.6, 0.2 M Lithium Sulfate, 18% PEG 3350, 10% 1,4 Butanediol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→38.4 Å / Num. obs: 27184 / % possible obs: 99.74 % / Redundancy: 2 % / Net I/σ(I): 2.82
Reflection shell% possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3qvo

3qvo


Resolution: 2→38.4 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1320 4.86 %
Rwork0.1784 --
obs0.1806 27184 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 16 342 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083156
X-RAY DIFFRACTIONf_angle_d0.9994287
X-RAY DIFFRACTIONf_dihedral_angle_d14.7371146
X-RAY DIFFRACTIONf_chiral_restr0.039489
X-RAY DIFFRACTIONf_plane_restr0.005564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.08010.2591420.20872816X-RAY DIFFRACTION98
2.0801-2.17480.24261230.18912866X-RAY DIFFRACTION100
2.1748-2.28940.25371680.17622860X-RAY DIFFRACTION100
2.2894-2.43290.26981370.182874X-RAY DIFFRACTION100
2.4329-2.62070.24191390.19272873X-RAY DIFFRACTION100
2.6207-2.88430.25131500.20072882X-RAY DIFFRACTION100
2.8843-3.30150.23431320.19252875X-RAY DIFFRACTION100
3.3015-4.15870.17961610.16112892X-RAY DIFFRACTION100
4.1587-38.41510.18511680.15562926X-RAY DIFFRACTION100

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